Mimulus Map
Ferreira, G. C.; Braga, P.; Oliveira, M.; Nomura, J. V.
June 17, 2019
Material and methods
To construct the map, we used the genotyping data of a population \(F_2\) consisted of 287 individuals, coming from the cross between Mimulus guttatus and Mimulus nasutus. As a result of the genotyping, 418 markers were obtained, of which 213 were codominant and 205 were dominant.
With the genotyping data, a genetic linkage map was constructed with software R (R CORE TEAM, 2018) and the “onemap” package (MARGARIDO et al., 2007).
data<-read_mapmaker(file = "m_feb06.raw")## --Read the following data:
## Type of cross: f2
## Number of individuals: 287
## Number of markers: 418
## Missing trait values:
## fl: 11
## fs: 19
## ft: 11
## ll: 20
## nv: 12
## pa: 35
## pal: 11
## pv: 12
## sa: 11
## sl: 11
## ss: 28
## tl: 11
## tp: 12
## tw: 11
## vi: 12
## ww: 11class(data)## [1] "onemap" "f2"plot(data)
plot_by_segreg_type(data)
Segregation test
Initially, the markers was filter based in segregation distortion (3:1 dominant markers and 1:2:1 codominant markers). The \(\chi^2\) test was used for each marker at 5% significance, corrected for multiple tests based on Bonferroni correction.
segreg_test <- test_segregation(data)
print(segreg_test)## Marker H0 Chi-square p-value % genot.
## 1 AA461 3:1 9.601212e+00 1.944490e-03 95.82
## 2 AA420 3:1 8.836364e-01 3.472076e-01 95.82
## 3 AA404 3:1 1.843636e+00 1.745253e-01 95.82
## 4 AA384 3:1 3.938182e+00 4.720177e-02 95.82
## 5 AA378 3:1 1.236485e+01 4.374931e-04 95.82
## 6 AA371C 1:2:1 5.392727e+00 6.745034e-02 95.82
## 7 AA361 3:1 4.810909e+00 2.828012e-02 95.82
## 8 AA341 3:1 2.241212e+00 1.343756e-01 95.82
## 9 AA311 3:1 5.441212e+00 1.966702e-02 95.82
## 10 AA280 3:1 3.404848e+00 6.500508e-02 95.82
## 11 AA277 3:1 3.503030e-01 5.539416e-01 95.82
## 12 AA270 3:1 5.441212e+00 1.966702e-02 95.82
## 13 AA268 3:1 1.484848e+00 2.230175e-01 95.82
## 14 AA246 3:1 1.090909e-02 9.168149e-01 95.82
## 15 AA208 3:1 9.818182e-02 7.540225e-01 95.82
## 16 AA173C 1:2:1 1.892000e+01 7.790659e-05 95.82
## 17 AA167 3:1 2.048485e-01 6.508354e-01 95.82
## 18 AA166C 1:2:1 3.296703e-02 9.836516e-01 95.12
## 19 AA163 3:1 8.757576e+00 3.083186e-03 95.82
## 20 AA158 3:1 1.212121e-03 9.722268e-01 95.82
## 21 AA137 3:1 1.387758e+01 1.951126e-04 95.82
## 22 AA100 3:1 5.441212e+00 1.966702e-02 95.82
## 23 AA95 3:1 7.575758e-01 3.840882e-01 95.82
## 24 AA66 3:1 5.939394e-02 8.074564e-01 95.82
## 25 BA497 3:1 8.901099e-01 3.454475e-01 95.12
## 26 BA449 3:1 1.011111e+01 1.473781e-03 95.12
## 27 BA445 3:1 4.250305e+00 3.924328e-02 95.12
## 28 BA416 3:1 1.397924e+01 1.848400e-04 95.12
## 29 BA400 3:1 4.407814e-01 5.067455e-01 95.12
## 30 BA394 3:1 5.813187e+00 1.590644e-02 95.12
## 31 BA387 3:1 2.496825e+01 5.828210e-07 95.12
## 32 BA384 3:1 9.890110e-02 7.531524e-01 95.12
## 33 BA374 3:1 8.010989e+00 4.649434e-03 95.12
## 34 BA372 3:1 8.901099e-01 3.454475e-01 95.12
## 35 BA334 3:1 1.026862e+00 3.108968e-01 95.12
## 36 BA314 3:1 1.173382e+00 2.787074e-01 95.12
## 37 BA311 3:1 1.495726e+00 2.213301e-01 95.12
## 38 BA301 3:1 2.697192e+00 1.005252e-01 95.12
## 39 BA222 3:1 2.063492e-01 6.496440e-01 95.12
## 40 BA220 3:1 6.155067e+00 1.310361e-02 95.12
## 41 BA214 3:1 2.567155e+01 4.047501e-07 95.12
## 42 BA210 3:1 4.846154e+00 2.770785e-02 95.12
## 43 BA196 3:1 2.933455e+01 6.089999e-08 95.12
## 44 BA175 3:1 5.813187e+00 1.590644e-02 95.12
## 45 BA172 3:1 5.982906e-02 8.067663e-01 95.12
## 46 BA158 3:1 2.257631e+00 1.329573e-01 95.12
## 47 BA153 3:1 1.450672e+01 1.396608e-04 95.12
## 48 BA145 3:1 8.901099e-01 3.454475e-01 95.12
## 49 BA129 3:1 1.729060e+01 3.207700e-05 95.12
## 50 BA125 3:1 4.846154e+00 2.770785e-02 95.12
## 51 BA117 3:1 1.098901e-02 9.165119e-01 95.12
## 52 BA113 3:1 9.890110e-02 7.531524e-01 95.12
## 53 BA75 3:1 1.329670e+00 2.488639e-01 95.12
## 54 BA69 3:1 5.813187e+00 1.590644e-02 95.12
## 55 BB327 3:1 1.784652e+01 2.394564e-05 96.86
## 56 BB281 3:1 1.731415e+00 1.882303e-01 96.86
## 57 BB279 3:1 5.875300e+00 1.535476e-02 96.86
## 58 BB259 3:1 5.875300e+00 1.535476e-02 96.86
## 59 BB218 3:1 2.997602e+00 8.338786e-02 96.86
## 60 BB216 3:1 4.316547e-02 8.354140e-01 96.86
## 61 BB210 3:1 8.868106e+00 2.901961e-03 96.86
## 62 BB208 3:1 2.537170e+00 1.111939e-01 96.86
## 63 BB198 3:1 2.115108e+00 1.458518e-01 96.86
## 64 BB190 3:1 1.386091e+00 2.390663e-01 96.86
## 65 BB186 3:1 4.609113e+00 3.180248e-02 96.86
## 66 BB182 3:1 2.115108e+00 1.458518e-01 96.86
## 67 BB176 3:1 6.565947e+00 1.039484e-02 96.86
## 68 BB167 3:1 4.796163e-03 9.447872e-01 96.86
## 69 BB124 3:1 3.465228e+01 3.941770e-09 96.86
## 70 BB122 3:1 4.609113e+00 3.180248e-02 96.86
## 71 BB119 3:1 3.884892e-01 5.330946e-01 96.86
## 72 BB102 3:1 5.803357e-01 4.461808e-01 96.86
## 73 CA497 3:1 1.739130e-01 6.766573e-01 96.17
## 74 CA415 3:1 4.830918e-01 4.870252e-01 96.17
## 75 CA399 3:1 9.468599e-01 3.305199e-01 96.17
## 76 CA392 3:1 9.468599e-01 3.305199e-01 96.17
## 77 CA384 3:1 9.352657e+00 2.226624e-03 96.17
## 78 CA378 3:1 4.946860e+00 2.613810e-02 96.17
## 79 CA315 3:1 1.932367e+00 1.644997e-01 96.17
## 80 CA305 3:1 4.830918e-01 4.870252e-01 96.17
## 81 CA297 3:1 2.782609e+00 9.529284e-02 96.17
## 82 CA289 3:1 1.565217e+00 2.109029e-01 96.17
## 83 CA283 3:1 6.956522e-01 4.042485e-01 96.17
## 84 CA279 3:1 1.739130e-01 6.766573e-01 96.17
## 85 CA267 3:1 3.408696e+01 5.270336e-09 96.17
## 86 CA264 3:1 3.741063e+01 9.569921e-10 96.17
## 87 CA261 3:1 1.739130e-01 6.766573e-01 96.17
## 88 CA238 3:1 8.521739e+00 3.509290e-03 96.17
## 89 CA233 3:1 4.830918e-01 4.870252e-01 96.17
## 90 CA228 3:1 1.932367e-02 8.894426e-01 96.17
## 91 CA226 3:1 2.104348e+01 4.489784e-06 96.17
## 92 CA220 3:1 9.468599e-01 3.305199e-01 96.17
## 93 CA217 3:1 8.521739e+00 3.509290e-03 96.17
## 94 CA210 3:1 1.236715e+00 2.661051e-01 96.17
## 95 CA198 3:1 3.265700e+00 7.074280e-02 96.17
## 96 CA196 3:1 1.932367e-02 8.894426e-01 96.17
## 97 CA174 3:1 3.265700e+00 7.074280e-02 96.17
## 98 CA167 3:1 4.946860e+00 2.613810e-02 96.17
## 99 CA152C 1:2:1 1.239130e+00 5.381784e-01 96.17
## 100 CA150 3:1 1.207729e+01 5.103960e-04 96.17
## 101 CA140 3:1 2.338164e+00 1.262382e-01 96.17
## 102 CA131 3:1 1.932367e+00 1.644997e-01 96.17
## 103 CA122 3:1 0.000000e+00 1.000000e+00 96.17
## 104 CA96 3:1 3.265700e+00 7.074280e-02 96.17
## 105 CA75 3:1 6.956522e-01 4.042485e-01 96.17
## 106 CB333 3:1 1.083032e-02 9.171147e-01 96.52
## 107 CB329 3:1 1.474128e+00 2.246956e-01 96.52
## 108 CB309 3:1 4.188929e+00 4.068879e-02 96.52
## 109 CB280 3:1 3.008424e-02 8.622992e-01 96.52
## 110 CB272 3:1 2.707581e-01 6.028237e-01 96.52
## 111 CB257 3:1 1.156438e+00 2.822055e-01 96.52
## 112 CB246 3:1 2.033694e-01 6.520148e-01 96.52
## 113 CB230 3:1 1.227557e+01 4.589261e-04 96.52
## 114 CB216 3:1 3.477738e-01 5.553761e-01 96.52
## 115 CB187 3:1 3.008424e-02 8.622992e-01 96.52
## 116 CB173 3:1 4.477738e+00 3.433915e-02 96.52
## 117 CB172 3:1 6.412756e+00 1.133034e-02 96.52
## 118 CB166 3:1 3.477738e-01 5.553761e-01 96.52
## 119 CB162 3:1 1.012034e+00 3.144161e-01 96.52
## 120 CB156 3:1 2.889290e+00 8.917021e-02 96.52
## 121 CB126 3:1 1.456077e-01 7.027686e-01 96.52
## 122 CB115 3:1 7.510229e+00 6.134958e-03 96.52
## 123 CB55 3:1 1.179422e+01 5.941478e-04 96.52
## 124 BD433 3:1 9.157161e+00 2.477466e-03 91.64
## 125 BD429 3:1 2.799747e+00 9.427921e-02 91.64
## 126 BD411 3:1 4.575412e-01 4.987753e-01 91.64
## 127 BD371 3:1 2.130545e+00 1.443894e-01 91.64
## 128 BD340 3:1 3.619899e+01 1.781632e-09 91.64
## 129 BD316C 1:2:1 1.023846e+01 5.980622e-03 90.59
## 130 BD292 3:1 1.065906e+00 3.018720e-01 91.64
## 131 BD286 3:1 6.210393e-02 8.032010e-01 91.64
## 132 BD270 3:1 5.030418e+00 2.490588e-02 91.64
## 133 BD263 3:1 1.927757e+00 1.650041e-01 91.64
## 134 BD251 3:1 5.030418e+00 2.490588e-02 91.64
## 135 BD243 3:1 1.140684e-02 9.149454e-01 91.64
## 136 BD242 3:1 2.966920e+01 5.124252e-08 91.64
## 137 BD239 3:1 1.735108e+00 1.877599e-01 91.64
## 138 BD209 3:1 3.560203e+00 5.918051e-02 91.64
## 139 BD179 3:1 1.026616e-01 7.486587e-01 91.64
## 140 BD175 3:1 6.704689e-01 4.128882e-01 91.64
## 141 BD173 3:1 1.505830e+01 1.042408e-04 91.64
## 142 BD170 3:1 1.552598e+00 2.127523e-01 91.64
## 143 BD169 3:1 6.704689e-01 4.128882e-01 91.64
## 144 BD143 3:1 1.380228e+00 2.400623e-01 91.64
## 145 BD130 3:1 3.168568e-02 8.587193e-01 91.64
## 146 BD115 3:1 1.065906e+00 3.018720e-01 91.64
## 147 BD100 3:1 4.721039e+01 6.376146e-12 91.64
## 148 BD99 3:1 9.239544e-01 3.364388e-01 91.64
## 149 BD68 3:1 5.589354e-01 4.546895e-01 91.64
## 150 BD55 3:1 1.217997e+00 2.697540e-01 91.64
## 151 BD189C 1:2:1 1.503042e+01 5.447361e-04 91.64
## 152 AA118C 1:2:1 3.360364e+01 5.047346e-08 95.82
## 153 AA153C 1:2:1 3.938182e+00 1.395837e-01 95.82
## 154 AA296C 1:2:1 5.392727e+00 6.745034e-02 95.82
## 155 AA346C 1:2:1 5.162963e+00 7.566183e-02 94.08
## 156 AA374C 1:2:1 8.832117e-01 6.430030e-01 95.47
## 157 AA454C 1:2:1 1.780727e+01 1.358939e-04 95.82
## 158 BA245C 1:2:1 1.240659e+01 2.022751e-03 95.12
## 159 BA279C 1:2:1 2.708955e+00 2.580821e-01 93.38
## 160 BA396C 1:2:1 9.904412e+00 7.067801e-03 94.77
## 161 CA183C 1:2:1 1.355072e+00 5.078667e-01 96.17
## 162 CA258C 1:2:1 1.410870e+01 8.636458e-04 96.17
## 163 CA389C 1:2:1 2.791304e+01 8.684796e-07 96.17
## 164 CB263C 1:2:1 2.342960e+00 3.099079e-01 96.52
## 165 BB103C 1:2:1 3.851986e+00 1.457310e-01 96.52
## 166 AAT217 1:2:1 9.379845e-01 6.256324e-01 89.90
## 167 AAT225 1:2:1 3.435510e+01 3.466446e-08 85.37
## 168 AAT261 1:2:1 1.156432e+01 3.082058e-03 83.97
## 169 AAT267 1:2:1 7.976580e+01 4.776137e-18 93.73
## 170 AAT240 1:2:1 9.856115e-01 6.109099e-01 96.86
## 171 AAT278 1:2:1 4.620818e+00 9.922067e-02 93.73
## 172 AAT39 1:2:1 1.007168e+00 6.043606e-01 97.21
## 173 AAT211 1:2:1 1.966543e+00 3.740853e-01 93.73
## 174 AAT222 1:2:1 3.507246e+00 1.731455e-01 96.17
## 175 AAT374 1:2:1 1.404255e+00 4.955299e-01 98.26
## 176 AAT233 1:2:1 3.468000e+01 2.946685e-08 78.40
## 177 AAT265 1:2:1 8.398885e+01 5.781672e-19 93.73
## 178 AAT367 1:2:1 2.048052e+01 3.570357e-05 80.49
## 179 AAT372 1:2:1 3.870968e-01 8.240300e-01 86.41
## 180 AAT296 1:2:1 2.572016e+00 2.763718e-01 84.67
## 181 AAT230 1:2:1 2.436508e+00 2.957461e-01 87.80
## 182 AAT272 1:2:1 4.953933e+01 1.748526e-11 62.02
## 183 AAT308 1:2:1 1.687952e+01 2.161022e-04 86.76
## 184 AG19 1:2:1 7.138996e+00 2.816999e-02 90.24
## 185 AAT364 1:2:1 5.770492e+00 5.584106e-02 85.02
## 186 AAT300 1:2:1 1.692308e+00 4.290620e-01 72.47
## 187 CYCB 1:2:1 5.741036e+00 5.666957e-02 87.46
## 188 AAT242 1:2:1 1.776448e+01 1.388329e-04 90.24
## 189 BC546 3:1 8.354752e+00 3.846799e-03 86.76
## 190 BC542 3:1 3.481928e+00 6.204243e-02 86.76
## 191 BC512 3:1 4.832664e-01 4.869465e-01 86.76
## 192 BC506 3:1 3.868809e-01 5.339435e-01 86.76
## 193 BC498 3:1 1.457831e+00 2.272755e-01 86.76
## 194 BC478 3:1 7.133869e+00 7.564135e-03 86.76
## 195 BC392 3:1 8.783133e+00 3.040287e-03 86.76
## 196 BC388 3:1 1.649398e+01 4.880489e-05 86.76
## 197 BC379 3:1 6.559572e-02 7.978608e-01 86.76
## 198 BC376 3:1 3.012048e-01 5.831281e-01 86.76
## 199 BC374 3:1 6.559572e-02 7.978608e-01 86.76
## 200 BC334 3:1 4.659973e+00 3.087367e-02 86.76
## 201 BC330 3:1 7.937082e+00 4.843188e-03 86.76
## 202 BC321 3:1 2.710843e+00 9.966829e-02 86.76
## 203 BC266 3:1 9.222222e+00 2.390952e-03 86.76
## 204 BC243 3:1 4.349398e+00 3.702204e-02 86.76
## 205 BC219 3:1 2.957162e+00 8.549789e-02 86.76
## 206 BC216 3:1 1.108568e+01 8.699710e-04 86.76
## 207 BC199 3:1 3.012048e-01 5.831281e-01 86.76
## 208 BC192 3:1 1.312048e+01 2.920849e-04 86.76
## 209 BC167 3:1 3.346720e-02 8.548448e-01 86.76
## 210 BC135 3:1 2.250335e+00 1.335855e-01 86.76
## 211 BC131 3:1 1.084337e-01 7.419344e-01 86.76
## 212 BC126 3:1 3.481928e+00 6.204243e-02 86.76
## 213 BC125 3:1 1.204819e-02 9.125963e-01 86.76
## 214 BC108 3:1 3.760375e+00 5.248081e-02 86.76
## 215 BC83 3:1 1.084337e-01 7.419344e-01 86.76
## 216 BC80 3:1 9.222222e+00 2.390952e-03 86.76
## 217 BC70 3:1 3.868809e-01 5.339435e-01 86.76
## 218 BC586C 1:2:1 3.701613e+00 1.571104e-01 86.41
## 219 BC526C 1:2:1 1.961044e+01 5.516285e-05 86.76
## 220 BC194C 1:2:1 5.530120e+00 6.297231e-02 86.76
## 221 BC128C 1:2:1 1.478313e+01 6.164297e-04 86.76
## 222 CC540 3:1 4.878049e-02 8.251991e-01 85.71
## 223 CC531 3:1 4.878049e-02 8.251991e-01 85.71
## 224 CC457 3:1 9.159892e-01 3.385303e-01 85.71
## 225 CC450 3:1 2.655827e-01 6.063105e-01 85.71
## 226 CC447 3:1 6.639566e+00 9.973821e-03 85.71
## 227 CC402 3:1 3.387534e+00 6.569113e-02 85.71
## 228 CC392 3:1 2.655827e-01 6.063105e-01 85.71
## 229 CC387 3:1 3.387534e+00 6.569113e-02 85.71
## 230 CC381 3:1 9.159892e-01 3.385303e-01 85.71
## 231 CC378 3:1 5.420054e-03 9.413119e-01 85.71
## 232 CC371 3:1 1.355014e-01 7.127949e-01 85.71
## 233 CC359 3:1 1.355014e-01 7.127949e-01 85.71
## 234 CC342 3:1 2.289973e+01 1.706759e-06 85.71
## 235 CC330 3:1 3.951220e+00 4.683741e-02 85.71
## 236 CC320 3:1 2.016802e+01 7.092882e-06 85.71
## 237 CC286 3:1 5.902439e+00 1.511993e-02 85.71
## 238 CC283 3:1 5.902439e+00 1.511993e-02 85.71
## 239 CC270 3:1 1.097561e+01 9.231887e-04 85.71
## 240 CC262 3:1 2.867209e+00 9.040154e-02 85.71
## 241 CC150 3:1 9.159892e-01 3.385303e-01 85.71
## 242 CC149 3:1 4.390244e-01 5.075937e-01 85.71
## 243 CC138 3:1 5.420054e-03 9.413119e-01 85.71
## 244 CC132 3:1 2.655827e-01 6.063105e-01 85.71
## 245 CC130 3:1 4.878049e-02 8.251991e-01 85.71
## 246 CC126 3:1 2.655827e-01 6.063105e-01 85.71
## 247 CC124 3:1 9.159892e-01 3.385303e-01 85.71
## 248 CC114 3:1 5.902439e+00 1.511993e-02 85.71
## 249 CC93 3:1 6.639566e+00 9.973821e-03 85.71
## 250 CC61 3:1 5.902439e+00 1.511993e-02 85.71
## 251 CC53 3:1 2.016802e+01 7.092882e-06 85.71
## 252 CC385C 1:2:1 7.553719e+00 2.289448e-02 84.32
## 253 CC338C 1:2:1 1.253061e+00 5.344428e-01 85.37
## 254 CC171C 1:2:1 4.560976e+00 1.022343e-01 85.71
## 255 AAT312 1:2:1 5.761905e+00 5.608133e-02 58.54
## 256 AAT283 1:2:1 1.061176e+01 4.962318e-03 59.23
## 257 LFY 1:2:1 4.300000e+00 1.164842e-01 83.62
## 258 AAT333 1:2:1 1.211732e+01 2.337533e-03 62.37
## 259 AP3 1:2:1 1.550943e+01 4.287155e-04 73.87
## 260 MgSTS17 1:2:1 1.118182e+01 3.731634e-03 91.99
## 261 MgSTS16 1:2:1 4.877477e+01 2.562667e-11 77.35
## 262 MgSTS18 1:2:1 5.403101e+00 6.710140e-02 89.90
## 263 MgSTS20 1:2:1 2.630566e+01 1.939985e-06 92.33
## 264 MgSTS21 1:2:1 1.095726e+01 4.175035e-03 81.53
## 265 MgSTS19 1:2:1 3.225984e+01 9.882440e-08 88.50
## 266 MgSTS24 1:2:1 3.481890e+01 2.748985e-08 88.50
## 267 MgSTS25 1:2:1 3.996226e+00 1.355909e-01 92.33
## 268 MgSTS22 1:2:1 2.360000e+00 3.072787e-01 95.82
## 269 MgSTS27 1:2:1 8.687732e+00 1.298622e-02 93.73
## 270 MgSTS26 1:2:1 1.088764e+01 4.322937e-03 93.03
## 271 MgSTS23 3:1 4.473358e-01 5.036029e-01 93.73
## 272 MgSTS28 1:2:1 1.405714e+01 8.861969e-04 97.56
## 273 MgSTS105 1:2:1 1.745247e+00 4.178538e-01 91.64
## 274 MgSTS120 1:2:1 2.551471e+00 2.792256e-01 94.77
## 275 MgSTS29 1:2:1 3.222936e+01 1.003423e-07 75.96
## 276 MgSTS38 1:2:1 1.955253e+01 5.678351e-05 89.55
## 277 MgSTS91 1:2:1 1.871642e+01 8.625445e-05 93.38
## 278 MgSTS93 1:2:1 1.628571e+01 2.908051e-04 92.68
## 279 MgSTS133 1:2:1 1.422963e+01 8.129712e-04 94.08
## 280 MgSTS58 1:2:1 3.362264e+00 1.861631e-01 92.33
## 281 MgSTS55 1:2:1 2.533333e+00 2.817693e-01 94.08
## 282 MgSTS40 1:2:1 5.156134e+00 7.592062e-02 93.73
## 283 MgSTS98 1:2:1 6.773438e+00 3.381947e-02 89.20
## 284 MgSTS45 1:2:1 1.200000e+01 2.478752e-03 93.38
## 285 MgSTS11 1:2:1 1.066935e+01 4.821465e-03 86.41
## 286 CYCA 1:2:1 7.848815e+01 9.047205e-18 73.52
## 287 aat356 1:2:1 8.664255e+01 1.533941e-19 81.88
## 288 MgSTS87 1:2:1 1.025312e+02 5.440289e-23 89.20
## 289 MgSTS132 1:2:1 1.645161e+00 4.392965e-01 86.41
## 290 MgSTS212 1:2:1 2.655738e+00 2.650415e-01 85.02
## 291 MgSTS228 1:2:1 6.853846e+00 3.248675e-02 90.59
## 292 MgSTS229 1:2:1 3.383459e+00 1.842007e-01 92.68
## 293 MgSTS234 1:2:1 9.381356e+00 9.180460e-03 82.23
## 294 MgSTS245 1:2:1 2.538710e+01 3.070874e-06 86.41
## 295 MgSTS308 1:2:1 1.016736e+00 6.014763e-01 83.28
## 296 MgSTS316 1:2:1 8.869565e-01 6.418002e-01 80.14
## 297 MgSTS323 1:2:1 5.236364e+00 7.293535e-02 76.66
## 298 MgSTS36 1:2:1 8.737052e+00 1.266990e-02 87.46
## 299 MgSTS43 1:2:1 3.481013e+00 1.754316e-01 82.58
## 300 MgSTS437 1:2:1 1.066923e+01 4.821764e-03 90.59
## 301 MgSTS48 1:2:1 6.739496e+00 3.439831e-02 82.93
## 302 MgSTS49 1:2:1 3.825000e+00 1.477106e-01 83.62
## 303 MgSTS59 1:2:1 8.692308e+00 1.295655e-02 81.53
## 304 MgSTS68 1:2:1 2.275862e+00 3.204814e-01 80.84
## 305 MgSTS70 1:2:1 2.430120e+01 5.285188e-06 86.76
## 306 MgSTS508 1:2:1 9.843137e-01 6.113065e-01 88.85
## 307 MgSTS527 1:2:1 5.127344e+01 7.347076e-12 89.20
## 308 MgSTS520 1:2:1 2.141107e+01 2.242053e-05 88.15
## 309 MgSTS529 1:2:1 2.781250e+00 2.489197e-01 89.20
## 310 MgSTS455 1:2:1 1.584746e+00 4.527692e-01 82.23
## 311 MgSTS468 1:2:1 4.483607e+00 1.062667e-01 85.02
## 312 MgSTS480 1:2:1 1.167939e+00 5.576803e-01 91.29
## 313 MgSTS474 1:2:1 6.666667e-02 9.672161e-01 88.85
## 314 MgSTS113 1:2:1 5.995745e+00 4.989311e-02 81.88
## 315 MgSTS106 1:2:1 2.062992e+00 3.564733e-01 88.50
## 316 MgSTS69 1:2:1 1.144355e+01 3.273897e-03 86.41
## 317 MgSTS56 1:2:1 2.927419e+00 2.313763e-01 86.41
## 318 MgSTS31 1:2:1 1.204918e+00 5.474638e-01 85.02
## 319 MgSTS95 1:2:1 1.115242e-02 9.944393e-01 93.73
## 320 MgSTS360 1:2:1 5.600415e+01 6.900070e-13 83.97
## 321 MgSTS262 1:2:1 3.137615e+00 2.082935e-01 75.96
## 322 MgSTS50 1:2:1 2.857820e+00 2.395699e-01 73.52
## 323 MgSTS75 1:2:1 2.188152e+01 1.772103e-05 73.52
## 324 MgSTS76 1:2:1 1.277228e+00 5.280238e-01 70.38
## 325 MgSTS341 1:2:1 2.353476e+01 7.753396e-06 65.16
## 326 MgSTS388 1:2:1 2.078341e+00 3.537480e-01 75.61
## 327 MgSTS330 1:2:1 2.188841e-01 8.963341e-01 81.18
## 328 MgSTS336 1:2:1 2.081481e+01 3.020789e-05 56.45
## 329 MgSTS332 1:2:1 1.614451e+01 3.120790e-04 60.28
## 330 MgSTS326 1:2:1 2.165217e+00 3.387108e-01 80.14
## 331 MgSTS282B 1:2:1 6.225806e+00 4.447166e-02 86.41
## 332 MgSTS282A 1:2:1 4.364807e+00 1.127702e-01 81.18
## 333 MgSTS255 1:2:1 2.870968e+00 2.380002e-01 86.41
## 334 MgSTS350 1:2:1 3.967213e+00 1.375722e-01 85.02
## 335 MgSTS348 1:2:1 2.462400e+01 4.497450e-06 87.11
## 336 MgSTS362 1:2:1 3.388186e+00 1.837659e-01 82.58
## 337 MgSTS358 1:2:1 4.129365e+01 1.079438e-09 87.80
## 338 MgSTS344 1:2:1 5.963563e+00 5.070243e-02 86.06
## 339 MgSTS471 1:2:1 6.378689e+01 1.408815e-14 63.76
## 340 MgSTS37 1:2:1 1.902954e+00 3.861703e-01 82.58
## 341 MgSTS34 1:2:1 4.777778e+00 9.173155e-02 84.67
## 342 MgSTS426 1:2:1 5.252336e+00 7.235518e-02 74.56
## 343 MgSTS453 1:2:1 5.073469e+00 7.912434e-02 85.37
## 344 MgSTS456 1:2:1 9.271493e+00 9.698863e-03 77.00
## 345 MgSTS457 1:2:1 4.439462e-01 8.009369e-01 77.70
## 346 MgSTS491 1:2:1 2.559740e+01 2.764360e-06 80.49
## 347 MgSTS492 1:2:1 3.904348e+00 1.419651e-01 80.14
## 348 MgSTS513 1:2:1 1.430380e+00 4.890992e-01 82.58
## 349 MgSTS509 1:2:1 6.892562e+00 3.186392e-02 84.32
## 350 MgSTS500 1:2:1 1.457627e+00 4.824811e-01 82.23
## 351 MgSTS430 1:2:1 2.863415e+00 2.389007e-01 71.43
## 352 MgSTS381 1:2:1 1.452991e-01 9.299266e-01 81.53
## 353 MgSTS398 1:2:1 6.949524e+01 8.115229e-16 73.17
## 354 MgSTS314 1:2:1 0.000000e+00 1.000000e+00 80.84
## 355 MgSTS380 1:2:1 1.049244e+02 1.644230e-23 82.93
## 356 MgSTS251 1:2:1 3.894410e+00 1.426723e-01 56.10
## 357 MgSTS351 1:2:1 1.062385e+01 4.932415e-03 75.96
## 358 MgSTS347 1:2:1 1.651685e+00 4.378658e-01 93.03
## 359 MgSTS320 1:2:1 1.620710e+01 3.024634e-04 58.89
## 360 MgSTS293 1:2:1 2.828358e+00 2.431251e-01 93.38
## 361 MgSTS263 1:2:1 3.205419e+01 1.095271e-07 70.73
## 362 MgSTS578 1:2:1 6.134454e-01 7.358546e-01 82.93
## 363 MgSTS571 1:2:1 9.609375e-01 6.184934e-01 89.20
## 364 MgSTS574B 1:2:1 7.079681e+00 2.901795e-02 87.46
## 365 MgSTS574a 1:2:1 1.051613e+01 5.205370e-03 86.41
## 366 MgSTS579 1:2:1 1.838095e+00 3.988988e-01 73.17
## 367 MgSTS638 1:2:1 5.733333e+00 5.688824e-02 83.62
## 368 MgSTS590 1:2:1 8.326996e-01 6.594495e-01 91.64
## 369 MgSTS589 1:2:1 1.469636e+00 4.795928e-01 86.06
## 370 MgSTS583 1:2:1 3.979412e+01 2.284637e-09 94.77
## 371 MgSTS586 1:2:1 1.337008e+01 1.249466e-03 88.50
## 372 MgSTS535 1:2:1 2.205882e-02 9.890312e-01 94.77
## 373 MgSTS537 1:2:1 6.092308e+00 4.754142e-02 90.59
## 374 MgSTS538 1:2:1 2.595420e-01 8.782965e-01 91.29
## 375 MgSTS536 1:2:1 1.609665e+00 4.471627e-01 93.73
## 376 MgSTS539 1:2:1 4.567164e+00 1.019185e-01 93.38
## 377 MgSTS631 1:2:1 2.152399e+01 2.118976e-05 94.43
## 378 MgSTS563 1:2:1 5.462094e+00 6.515105e-02 96.52
## 379 MgSTS562 1:2:1 7.378161e+01 9.517593e-17 90.94
## 380 MgSTS561 1:2:1 9.463296e+01 2.823021e-21 93.03
## 381 MgSTS558 1:2:1 1.074820e+01 4.635085e-03 96.86
## 382 MgSTS548 1:2:1 1.852632e+01 9.485531e-05 79.44
## 383 MgSTS419 1:2:1 1.230769e-01 9.403168e-01 90.59
## 384 MgSTS611 1:2:1 1.416058e+00 4.926141e-01 95.47
## 385 MgSTS632 1:2:1 7.826087e-01 6.761743e-01 96.17
## 386 MgSTS609 1:2:1 1.564286e+00 4.574248e-01 97.56
## 387 MgSTS600 1:2:1 9.175182e+00 1.017734e-02 95.47
## 388 MgSTS565 1:2:1 1.378182e+00 5.020323e-01 95.82
## 389 MgSTS606 1:2:1 9.960000e+00 6.874063e-03 95.82
## 390 MgSTS577 1:2:1 1.300730e+01 1.497962e-03 95.47
## 391 MgSTS425 1:2:1 1.951095e+01 5.797640e-05 95.47
## 392 MgSTS438 1:2:1 8.078740e+00 1.760856e-02 88.50
## 393 MgSTS435 1:2:1 2.829801e+01 7.164147e-07 52.61
## 394 MgSTS494 1:2:1 1.079892e+02 3.551672e-24 97.21
## 395 MgSTS477 1:2:1 1.908425e+00 3.851153e-01 95.12
## 396 MgSTS483 1:2:1 6.404317e+01 1.239377e-14 96.86
## 397 MgSTS383 1:2:1 5.168498e+00 7.545272e-02 95.12
## 398 MgSTS504A 1:2:1 3.579926e+00 1.669664e-01 93.73
## 399 MgSTS504B 1:2:1 7.711111e+00 2.116184e-02 94.08
## 400 MgSTS504C 1:2:1 1.133333e+00 5.674137e-01 94.08
## 401 MgSTS545 1:2:1 1.298851e+00 5.223459e-01 90.94
## 402 MgSTS542A 1:2:1 2.238462e+00 3.265309e-01 90.59
## 403 MgSTS542B 1:2:1 1.249027e+00 5.355218e-01 89.55
## 404 MgSTS598 1:2:1 7.442623e+00 2.420221e-02 85.02
## 405 MgSTS441 1:2:1 5.146667e+00 7.628085e-02 52.26
## 406 MgSTS620 1:2:1 4.080916e+01 1.375319e-09 91.29
## 407 MgSTS104 1:2:1 7.349057e+00 2.536137e-02 73.87
## 408 MgSTS511 1:2:1 4.258427e+00 1.189308e-01 93.03
## 409 MgSTS621 1:2:1 2.014925e-01 9.041624e-01 93.38
## 410 MgSTS622 1:2:1 1.635294e+00 4.414692e-01 88.85
## 411 MgSTS459 1:2:1 3.283582e-01 8.485900e-01 93.38
## 412 MgSTS220 1:2:1 2.977695e+00 2.256325e-01 93.73
## 413 MgSTS214 1:2:1 1.342205e+00 5.111446e-01 91.64
## 414 MgSTS467 1:2:1 8.253219e+00 1.613750e-02 81.18
## 415 MgSTS470 1:2:1 1.096887e+01 4.150876e-03 89.55
## 416 MgSTS599 1:2:1 1.429644e+01 7.862613e-04 88.15
## 417 MgSTS431 1:2:1 7.651376e+00 2.180343e-02 75.96
## 418 MgSTS440 1:2:1 1.064516e+00 5.872774e-01 86.41Bonferroni_alpha(segreg_test)## [1] 0.0001196172plot(segreg_test)
(no_dist<-select_segreg(segreg_test,distorted = F,numbers = T))## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 17 18
## [18] 19 20 21 22 23 24 25 26 27 28 29 30 32 33 34 35 36
## [35] 37 38 39 40 42 44 45 46 47 48 50 51 52 53 54 56 57
## [52] 58 59 60 61 62 63 64 65 66 67 68 70 71 72 73 74 75
## [69] 76 77 78 79 80 81 82 83 84 87 88 89 90 92 93 94 95
## [86] 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112
## [103] 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 129 130
## [120] 131 132 133 134 135 137 138 139 140 142 143 144 145 146 148 149 150
## [137] 151 153 154 155 156 157 158 159 160 161 162 164 165 166 168 170 171
## [154] 172 173 174 175 179 180 181 183 184 185 186 187 188 189 190 191 192
## [171] 193 194 195 197 198 199 200 201 202 203 204 205 206 207 208 209 210
## [188] 211 212 213 214 215 216 217 218 220 221 222 223 224 225 226 227 228
## [205] 229 230 231 232 233 235 237 238 239 240 241 242 243 244 245 246 247
## [222] 248 249 250 252 253 254 255 256 257 258 259 260 262 264 267 268 269
## [239] 270 271 272 273 274 278 279 280 281 282 283 284 285 289 290 291 292
## [256] 293 295 296 297 298 299 300 301 302 303 304 306 309 310 311 312 313
## [273] 314 315 316 317 318 319 321 322 324 326 327 329 330 331 332 333 334
## [290] 336 338 340 341 342 343 344 345 347 348 349 350 351 352 354 356 357
## [307] 358 359 360 362 363 364 365 366 367 368 369 371 372 373 374 375 376
## [324] 378 381 383 384 385 386 387 388 389 390 392 395 397 398 399 400 401
## [341] 402 403 404 405 407 408 409 410 411 412 413 414 415 416 417 418(dist<-select_segreg(segreg_test,distorted = T,numbers = T))## [1] 16 31 41 43 49 55 69 85 86 91 128 136 141 147 152 163 167
## [18] 169 176 177 178 182 196 219 234 236 251 261 263 265 266 275 276 277
## [35] 286 287 288 294 305 307 308 320 323 325 328 335 337 339 346 353 355
## [52] 361 370 377 379 380 382 391 393 394 396 406After filtering, 15% of markers with segregation distortion were identified. These markers were not used in the construction of the linkage map.
Grouping
The recombination fraction for all pairs of markers was estimated using the “rf_2pts” function. A sequence (“make_seq”) was created containing all markers that did not show segregation distortion. Then the markers were grouped using the “group” function based on the maximum recombination fraction of 0.3 and the maximum LOD calculated by the “suggest_lod” function (5.43).
twopts<-rf_2pts(data)## Computing 87153 recombination fractions:
##
## 0% ........................................... 100%mark <- make_seq(twopts, no_dist)
(LOD_sug <- suggest_lod(data))## [1] 5.429707LGs <- group(mark, LOD = LOD_sug, max.rf = 0.3)## Selecting markers:
## group 1
## .......
## group 2
## ......................
## group 3
## ............................................................
## .......................
## group 4
## .......................................
## group 5
## ...............
## group 6
## ...................................................
## group 7
## ................................
## group 8
## ..........................
## group 9
## .............
## group 10
## ......
## group 11
## ........................
## group 12
## .....................
## group 13
## ......
## group 14
## ...Ordering
The clustering resulted in 14 linkage groups. We use the command “order_seq” to find the most likely order within each formed link group. The “doParallel” package was used to parallelize the process and optimize the analysis time.
cl<-makeCluster(detectCores()-1)
registerDoParallel(cl)
seq<-foreach (i = 1:LGs$n.groups,.packages = "onemap") %dopar% {
assign("data",data,envir = .GlobalEnv)
assign("twopts",twopts,envir = .GlobalEnv)
make_seq(order_seq(input.seq= make_seq(LGs,i),twopt.alg ="rcd"), "force")
}
stopCluster(cl)
rm("cl")
plot<-list()
for (i in 1:LGs$n.groups){
plot[[i]]<-rf_graph_table(seq[[i]],main = paste("Group",i),mrk.axis = "numbers")
}Removing Markers
Markers that presented poor positioning in each group were removed based on the graphical analysis. These markers were excluded during the mapping process, using the “drop_mark” function.
plot[[1]]
plot[[2]]
rf_graph_table(map(drop_marker(seq[[2]],c(252,50,2,245,90,296,84))))
out_mark<-c(252,50,2,245,90,296,84)
plot[[3]]
rf_graph_table(map(drop_marker(seq[[3]],c(56,405,237,217,211,221,131,125,115,64,229,130,25,149))))
out_mark<-c(out_mark,56,405,237,217,211,221,131,125,115,64,229,130,25,149)
plot[[4]]
rf_graph_table(map(drop_marker(seq[[4]],c(4,293,111,239,126,77,146))))
out_mark<-c(out_mark,4,293,111,239,126,77,146)
plot[[5]]
rf_graph_table(map(drop_marker(seq[[5]],c(65))))
out_mark<-c(out_mark,65)
plot[[6]]
rf_graph_table(map(drop_marker(seq[[6]],c(181,20,246,6,204,312,213,150))))
out_mark<-c(out_mark,181,20,246,6,204,312,213,150)
plot[[7]]
plot[[8]]
rf_graph_table(map(drop_marker(seq[[8]],c(87,17,222,93))))
out_mark<-c(out_mark,87,17,222,93)
plot[[9]]
plot[[10]]
out_mark<-c(out_mark,seq[[10]]$seq.num)
plot[[11]]
rf_graph_table(map(drop_marker(seq[[11]],c(30,44))))
out_mark<-c(out_mark,30,44)
plot[[12]]
rf_graph_table(map(drop_marker(seq[[12]],c(117))))
out_mark<-c(out_mark,117)
plot[[13]]
plot[[14]]
After the markers were removed, the grouping and sorting were performed again. Fifteen groups were obtained and analyzed again, removing markers that presented a poor positioning from the linkage mapping. Group 15 was completely removed for presenting only 3 non-informative marks.
mark<-(no_dist)[!no_dist%in%out_mark]
mark <- make_seq(twopts, mark)
LGs <- group(mark, LOD = LOD_sug, max.rf = 0.3)## Selecting markers:
## group 1
## .......
## group 2
## ..................
## group 3
## ..............
## group 4
## ...................
## group 5
## ...........................................
## group 6
## ................................
## group 7
## ................................
## group 8
## .............
## group 9
## ................................
## group 10
## ......................
## group 11
## ....................
## group 12
## ...............
## group 13
## ......
## group 14
## ......................
## group 15
## ...cl<-makeCluster(detectCores()-1)
registerDoParallel(cl)
seq<-foreach (i = 1:LGs$n.groups,.packages = "onemap") %dopar% {
assign("data",data,envir = .GlobalEnv)
assign("twopts",twopts,envir = .GlobalEnv)
make_seq(order_seq(input.seq= make_seq(LGs,i),twopt.alg ="rcd"), "force")
}
stopCluster(cl)
rm("cl")
plot<-list()
for (i in 1:LGs$n.groups){
plot[[i]]<-rf_graph_table(seq[[i]],main = paste("Group",i),mrk.axis = "numbers")
}
plot[[1]]
plot[[2]]
plot[[3]]
plot[[4]]
rf_graph_table(map(drop_marker(seq[[4]],c(116,71,168))))
seq[[4]]<-map(drop_marker(seq[[4]],c(116,71,168)))
out_mark<-c(out_mark,116,71,168)
plot[[5]]
rf_graph_table(map(drop_marker(seq[[5]],c(51,12))))
seq[[5]]<-map(drop_marker(seq[[5]],c(51,12)))
out_mark<-c(out_mark,51,12)
plot[[6]]
rf_graph_table(map(drop_marker(seq[[6]],c(46))))
seq[[6]]<-map(drop_marker(seq[[6]],c(46)))
out_mark<-c(out_mark,46)
plot[[7]]
rf_graph_table(map(drop_marker(seq[[7]],c(81,145))))
seq[[7]]<-map(drop_marker(seq[[7]],c(81,145)))
out_mark<-c(out_mark,81,145)
plot[[8]]
plot[[9]]
rf_graph_table(map(drop_marker(seq[[9]],c(256,108,408,329,124))))
seq[[9]]<-map(drop_marker(seq[[9]],c(256,108,408,329,124)))
out_mark<-c(out_mark,256,108,408,329,124)
plot[[10]]
plot[[11]]
plot[[12]]
plot[[13]]
plot[[14]]
rf_graph_table(map(drop_marker(seq[[14]],c(205,203,248,242))))
seq[[14]]<-map(drop_marker(seq[[14]],c(205,203,248,242)))
out_mark<-c(out_mark,205,203,248,242)
plot[[15]]
seq<-seq[-15]
draw_map2(seq[1:7],output = "m_feb06.jpeg",tag = "all",num = T,
group.names = paste("Group",1:7),cex.label = .75)## Completed
## Output file: /home/getulio/m_feb06/m_feb06(6).jpegdraw_map2(seq[8:14],output = "m_feb06.jpeg",tag = "all",num = T,
group.names = paste("Group",8:14),lim = 240,cex.label = .75)## Completed
## Output file: /home/getulio/m_feb06/m_feb06(7).jpeg
##Literature Cited
Margarido G, de Souza A, Garcia A (2007). “OneMap: software for genetic mapping in outcrossing species.” Hereditas.
R Core Team (2018). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
Microsoft Corporation and Steve Weston (2018). doParallel: Foreach Parallel Adaptor for the ‘parallel’ Package.